Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_016914362.1 HSS18214_RS0105820 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000275725.1:WP_016914362.1
Length = 880
Score = 1342 bits (3474), Expect = 0.0
Identities = 676/879 (76%), Positives = 751/879 (85%), Gaps = 12/879 (1%)
Query: 1 MNSANRKPLP-----GTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLT 55
MN+ RKPLP G +D+FD R AVE IQPGAY +LPYTSRVLAE LVRRCDPA LT
Sbjct: 1 MNTNYRKPLPNVSVAGAPVDFFDTRQAVEEIQPGAYAQLPYTSRVLAEQLVRRCDPALLT 60
Query: 56 DSLLQLVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQ 115
D+L QL+ RK++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDPAKVNPVVP Q
Sbjct: 61 DALKQLIERKQELDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQ 120
Query: 116 LIVDHSLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQI 175
LIVDHSLAVE GF+ DAF KNR +EDRRN+DRFHFI+WTK AF+NVDVIPPGNGIMHQI
Sbjct: 121 LIVDHSLAVEHAGFEKDAFEKNRQVEDRRNDDRFHFINWTKLAFENVDVIPPGNGIMHQI 180
Query: 176 NLEKMSPVIHA---DNGV--AYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRAS 230
NLEKMSPV+ + GV AYPDTCVGTDSHTP VDALGVI++GVGGLEAE+VMLGRAS
Sbjct: 181 NLEKMSPVVQCRPDEQGVQVAYPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRAS 240
Query: 231 WMRLPDIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRAT 290
MRLPDIVGVELTGK QPGIT TD+VLA+TEFLR+E+VVGAYLEF GEGA +L++GDRAT
Sbjct: 241 MMRLPDIVGVELTGKLQPGITGTDMVLAITEFLRRERVVGAYLEFFGEGADALSVGDRAT 300
Query: 291 ISNMAPEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERV 350
ISNM PEYGATAAMF+ID+QTIDYL+LTGR DEQ+ LV+ YA+ GLWAD L YER+
Sbjct: 301 ISNMTPEYGATAAMFYIDDQTIDYLKLTGRDDEQVALVKAYAQHTGLWADDLTQVVYERI 360
Query: 351 LKFDLSSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITS 410
L+FDLSSV R +AGPSNPH LPT+ LA+RGIAV LDKA +EA G MPDGAVIIAAITS
Sbjct: 361 LRFDLSSVTRTLAGPSNPHAHLPTTELAKRGIAVGLDKAREEEAAGKMPDGAVIIAAITS 420
Query: 411 CTNTSNPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGF 470
CTNTSNPRN++AA L+ARNAN GL RKPWVK+SLAPGSK V++YLEEA L+ +LE LGF
Sbjct: 421 CTNTSNPRNMVAAGLIARNANRLGLTRKPWVKTSLAPGSKTVKMYLEEAELMGELEALGF 480
Query: 471 GIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 530
G+VA+ACTTCNGMSGAL+P IQ+EII RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL
Sbjct: 481 GVVAYACTTCNGMSGALEPSIQEEIIRRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 540
Query: 531 VVAYAIAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPM 590
VVAYAIAGTIRFDIE+DVLG D G PV LKDIWP D EIDAIV SVKPEQFR+ Y PM
Sbjct: 541 VVAYAIAGTIRFDIEQDVLGHDAQGNPVTLKDIWPEDSEIDAIVKASVKPEQFRETYIPM 600
Query: 591 FAITAASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSP 650
F + +G VSPLY+WRPQSTYIRRPPYWEG +A ER LK +RPLA+L DNITTDHLSP
Sbjct: 601 FDLDKRAGPQVSPLYEWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSP 660
Query: 651 SNAIMLNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVK 709
SNAI+++SAAGEYL MGLPEEDFNSYATHRGDHLTAQRAT ANP L NEM + G+V
Sbjct: 661 SNAILMDSAAGEYLHAMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVHDEQGKVM 720
Query: 710 KGSLARIEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIV 769
+GSLARIEPEG V RMWEAIETYM RKQPLIIIAGADYGQGSSRDWAAKGV LAGVE IV
Sbjct: 721 QGSLARIEPEGTVTRMWEAIETYMARKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIV 780
Query: 770 AEGFERIHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNG 829
AEGFERIHRTNL+GMGV+PL+F+ G R TL LDGTE YDV G PRA LTLV++R+ G
Sbjct: 781 AEGFERIHRTNLVGMGVMPLQFEEGTTRKTLALDGTEIYDVEGTPAPRAQLTLVIHRQQG 840
Query: 830 ERVEVPVTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
VPV CRLD+ EEV+IY AGGVL FAQDFLESS A
Sbjct: 841 AVERVPVVCRLDTAEEVTIYSAGGVLQRFAQDFLESSAA 879
Lambda K H
0.318 0.135 0.398
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2155
Number of extensions: 85
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 869
Length of database: 880
Length adjustment: 42
Effective length of query: 827
Effective length of database: 838
Effective search space: 693026
Effective search space used: 693026
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate WP_016914362.1 HSS18214_RS0105820 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR02333.hmm
# target sequence database: /tmp/gapView.4023035.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02333 [M=858]
Accession: TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1710.9 0.1 0 1710.7 0.1 1.0 1 NCBI__GCF_000275725.1:WP_016914362.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000275725.1:WP_016914362.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1710.7 0.1 0 0 1 858 [] 2 875 .. 2 875 .. 0.98
Alignments for each domain:
== domain 1 score: 1710.7 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpg.....tdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreld 68
nt+yrk+lp+ + +d+fd+r+ave+i+pgay++lpytsrvlae+lvrr+dp+ l+++lkqlierk+eld
NCBI__GCF_000275725.1:WP_016914362.1 2 NTNYRKPLPNvsvagAPVDFFDTRQAVEEIQPGAYAQLPYTSRVLAEQLVRRCDPALLTDALKQLIERKQELD 74
899*****9766666889******************************************************* PP
TIGR02333 69 fpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraied 141
fpwyparvvchdilgqtalvdlaglrdaiaekggdpa+vnpvv+tqlivdhslave +gf++dafeknr++ed
NCBI__GCF_000275725.1:WP_016914362.1 75 FPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDHSLAVEHAGFEKDAFEKNRQVED 147
************************************************************************* PP
TIGR02333 142 rrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvk...eg..vafpdtlvgtdshtphvdalg 209
rrn+drfhfinwtk af+nvdvip+gngimhqinlekmspvvq++ +g va+pdt+vgtdshtp vdalg
NCBI__GCF_000275725.1:WP_016914362.1 148 RRNDDRFHFINWTKLAFENVDVIPPGNGIMHQINLEKMSPVVQCRpdeQGvqVAYPDTCVGTDSHTPMVDALG 220
*******************************************8633345447******************** PP
TIGR02333 210 viaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakal 282
vi++gvggleae+vmlgras+mrlpdivgveltgk qpgit td+vla+teflr+e+vv+ayleffgega al
NCBI__GCF_000275725.1:WP_016914362.1 221 VISVGVGGLEAESVMLGRASMMRLPDIVGVELTGKLQPGITGTDMVLAITEFLRRERVVGAYLEFFGEGADAL 293
************************************************************************* PP
TIGR02333 283 tlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdls 355
++gdratisnmtpeygataamf+id+qtidylkltgr++eqv+lv++ya+ +glwad+l + vyer+l+fdls
NCBI__GCF_000275725.1:WP_016914362.1 294 SVGDRATISNMTPEYGATAAMFYIDDQTIDYLKLTGRDDEQVALVKAYAQHTGLWADDLTQVVYERILRFDLS 366
************************************************************************* PP
TIGR02333 356 svvrnlagpsnpharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarn 424
sv+r+lagpsnpha l+t++la +gia +++ ea g+mpdgaviiaaitsctntsnprn+vaagl+arn
NCBI__GCF_000275725.1:WP_016914362.1 367 SVTRTLAGPSNPHAHLPTTELAKRGIAVGLDKareeEAAGKMPDGAVIIAAITSCTNTSNPRNMVAAGLIARN 439
*************************99755433333999********************************** PP
TIGR02333 425 anklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlya 497
an+lgl+rkpwvk+slapgsk+vk+yleea+l+ ele lgfg+va+acttcngmsgal+p iq+eii rdlya
NCBI__GCF_000275725.1:WP_016914362.1 440 ANRLGLTRKPWVKTSLAPGSKTVKMYLEEAELMGELEALGFGVVAYACTTCNGMSGALEPSIQEEIIRRDLYA 512
************************************************************************* PP
TIGR02333 498 tavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavva 570
tavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdie+dvlg+da+g+++ lkdiwp d eida+v+
NCBI__GCF_000275725.1:WP_016914362.1 513 TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEQDVLGHDAQGNPVTLKDIWPEDSEIDAIVK 585
************************************************************************* PP
TIGR02333 571 aavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhl 642
a+vkpeqfr+ yipmfdl+ a+ +vsply+wrp+styirrppyweg +a er lkgmrpla+l+dnittdhl
NCBI__GCF_000275725.1:WP_016914362.1 586 ASVKPEQFRETYIPMFDLDkRAGPQVSPLYEWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHL 658
*******************7789************************************************** PP
TIGR02333 643 spsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepeg 714
spsnail+dsaageyl+ mglpeedfnsyathrgdhltaqrat+anpklfnemv+++ gkv qgslariepeg
NCBI__GCF_000275725.1:WP_016914362.1 659 SPSNAILMDSAAGEYLHAMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVHDEqGKVMQGSLARIEPEG 731
*******************************************************999*************** PP
TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkp 787
+vtrmweaietym rkqpliiiagadygqgssrdwaakgv lagveaivaegferihrtnlvgmgv+pl+f
NCBI__GCF_000275725.1:WP_016914362.1 732 TVTRMWEAIETYMARKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRTNLVGMGVMPLQFEE 804
************************************************************************* PP
TIGR02333 788 gtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
gt rktlaldgte+ydv g+ +pra+ltlv++r++g vpv crldtaeev++y aggvlqrfaqdfle
NCBI__GCF_000275725.1:WP_016914362.1 805 GTTRKTLALDGTEIYDVEGTPAPRAQLTLVIHRQQGAVERVPVVCRLDTAEEVTIYSAGGVLQRFAQDFLE 875
*********************************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (880 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 35.27
//
[ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory